(A) Peaks were called against control CHART-seq experiments and input DNA. We consider only the 1427 peaks common to both comparisons (Supplementary File 5). (B) Sequencing of Dali bound DNA reveals focal peaks, including those at the promoter of Ache, E2f2, and Hmgb2. (C and D) Dali peaks are broadly distributed across the mouse genome (C) but are particularly enriched in 5′ UTRs and gene promoters (D). Red arrowheads in (C) mark the Dali locus. (E) A third of Dali peaks are situated within 5 kb of a TSS. (F) Dali-bound loci are enriched in active chromatin marks (H3K4me3, H3K27ac, PolII), DNase I hypersensitivity regions, enhancers and CpG islands annotations (CGI), and CTCF-bound regions, while being depleted of gene body marks (H3K36me3) and repressive chromatin marks (H3K9me3 and H3K27me3). (G) Representative categories from GO analysis of genes associated with Dali binding sites (within 1 Mb) include gene expression, cell cycle, signalling, synaptic transmission and cytoskeleton organization among others. Categories marked with an asterisk (*) are significantly enriched also among genes associated with peaks within 10 kb of a TSS, with two asterisks (**)—among genes with peaks within 100 kb (Supplementary File 5). (H) The intersection of genes proximal (<1 Mb) to Dali peaks, regulated by Dali and changing expression upon Pou3f3 (10% FDR) knockdown identifies those both bound and regulated by Dali, as well as genes regulated by both Dali and Pou3f3 and directly bound by Dali.